/**
 * File: FileLocations.java
 * Created by: mhaimel
 * Created on: 16 Jul 2009
 * CVS:  $Id: FileLocations.java,v 1.4 2009/10/09 14:44:02 mhaimel Exp $
 */
package uk.ac.ebi.curtain.configuration;

import java.io.File;

import uk.ac.ebi.curtain.utils.data.ReadType;

/**
 * @author mhaimel
 *
 */
public interface FileLocations {

	File getConfigurationInformation();
	File getWorkingDir();
	File getMaqDir();
	File getBucketDir();
//	File getContigDir();
	File getSuperContigFile();
	
	File getGraph(String type);
	File getGraphStatistic(String type);
	File getLastGraph();

	File getEntryFilePosition(ReadType type);
	File getEntryMapPosition(ReadType type);
	File getSequenceBoxMapping(ReadType type,Integer category,boolean fullMatch);
//	File getMappedMapData();
	File getMappedData(ReadType type);
	
	File getIndexFile(ReadType type);
	
}
